Project description:Bulk RNA-seq data of Lin-CD34+ hematopoietic stem and progenitor cells derived from bone marrow of healthy donors and untreated aplastic anemia patients
Project description:Targeted genotyping-based identification of donor- and recipient-derived cells to resolve the origin of myelodysplastic syndrome (MDS) following allogeneic stem cell transplantation in the context of aplastic anemia (AA).
Project description:We identified three fibroblast cultures derived from aplastic anemia patients in the Japanese Cancer Research Resources Bank (JCRB) Cell Bank that showed high levels of sister chromatid exchanges (SCEs) in PHA-stimulated lymphoblasts. To elucidate the genetic basis of the high SCE, we carried out whole exome sequencing of these samples. Subsequently, germline variants were analysed for these patients.
Project description:CD3+ T cells derived from bone marrow aspirates and peripheral blood samples of newly diagnosed AA patients and healthy volunteers were analysed using Affymetrix HG_U133A GeneChips. Additionally, two patients were studied after achieving a partial remission (post-Therapy). Experiment Overall Design: Altogether, we analysed 8 different samples. Pool I contained three female and one male patients, 19 to 70 years old, suffering from (severe) aplastic anemia. From these four donors, samples derived from bone marrow aspirates and from peripheral blood, were pooled on total-RNA basis. Pool II consisted of additional two patients, one male (64 years old) and one female (70 years old). From both donors, total-RNA was extracted and pooled from CD3+ T cells derived either from bone marrow or peripheral blood, each prior and post therapy. Healthy control pools included three donors for the peripheral blood sample and two donors for bone marrow derived T cells.
Project description:Fanconi anemia (FA) is a rare inherited disease complicated by aplastic anemia. There is evidence that hematopoietic stem cells have lost self replicative capacity and undergo apoptosis when exposed to inhibitory cytokines including interferon gamma and tumor necrosis factor-alpha. We used gene expression microarrays to identify transcriptomal differences between bone marrow cells from normal volunteers and from children and adults with Fanconi anemia
Project description:We generated a paired snRNA-seq (n= 15) and spatial transcriptomics (n=19) dataset from subcortical chronic active and chronic inactive MS lesions, identifying spatial niches and key cell interactions driving inflammation and disease progression at the lesion rim. This repository offers access to all the trancriptomics data that was used in the paper. It includes, all FASTQ files for both transcriptomics, along with the necessary files for running spatial transcriptomic samples (H&E images and JSON files), as well as the curated atlas, all derived cell subtype atlases from the main atlas and all curated ST slides.